Past Awardee

Patchwork Molecular Dynamics: A New Paradigm for Hardware-Accelerated Large-Scale All-Atom Simulations of Biological Systems

Aleksei Aksimentiev

College: Engineering
Award year: 2015-2016

The project will explore new hardware architectures for implementing a molecular dynamics code to enable millisecond-timescale simulations of large biomolecular systems. The idea is to model individual biomolecules in the conventional, all-atom manner, but then to use a different algorithm that will take into account the distance between molecules to enable new approximations that do not require all-atom communications. This method will take advantage of the fact that forces between proteins decay exponentially with separation.